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The trillions of microbes that live in your gut help digest your food and protect you from potentially harmful bacteria, fungi, and viruses. They also make some vitamins for you. The more diverse this community, the better it is for your health.

So how do you boost diversity in your gut microbiome? Diet and medications can make a difference, but not always in predictable ways: Fruits and veggies, for instance, are good for the gut — but so is coffee. Frequent snacking isn’t helpful. Eating yogurt is.


That analysis comes from two large studies, the Flemish Gut Flora Project and the LifeLines-DEEP project, that set out to identify factors that affect the hundreds of microbial species living in the average person’s gut. Their analyses were published Thursday in Science.

Among the findings:

Good foods for boosting the gut microbiome

  • Fruit and vegetables
  • Yogurt
  • Coffee
  • Tea
  • Red wine

Bad habits that hurt the microbial ecosystem

  • A high-calorie diet
  • A high-carbohydrate diet
  • Sugar-sweetened beverages
  • Frequent snacks
  • Whole milk

Diet isn’t the most important factor, however: In the Flemish Gut Flora Project, medications had the biggest influence on gut microbiome diversity. Antibiotics, proton-pump inhibitors (taken to ease heartburn), and metformin (a common diabetes drug) were all linked to lower diversity. So were diseases such as ulcerative colitis, inflammatory bowel disease, and chronic fatigue syndrome.


Younger people, women, nonsmokers, and those with more red blood cells or harder stools (as opposed to loose stools) tended to have more diverse microbiomes.

Keep in mind that these reports describe association studies that looked at gut microbiome diversity in populations. How their results translate to individuals remains to be seen.

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